[R-SIG-Mac] source compile R -- emutls_get_address | libgomp.1.dylib

[Gustavo Carvalho]

I know this is not exactly what you asked, but may I suggest homebrew?

http://mxcl.github.com/homebrew/

It is a package manager for the Mac, but it compiles almost everything
from source. It can also handle dependencies.

To edit the flags you want to pass to the compiler, you need to edit a
formula, which is a set of instructions on how to compile and install
a given package:

https://github.com/mxcl/homebrew/blob/master/Library/Formula/r.rb

Once you have edited the formula, if the defaults were not
satisfactory, you just need to type sudo brew install r in a terminal
and homebrew will take care of the rest.

Best,

Gustavo

On Thu, Jul 7, 2011 at 10:41 PM, Benton, Paul
<hpaul.benton08 at imperial.ac.uk> wrote:
> Dear R mac people,
>
> I have some code that I would like to run as fast as possible. After reading some blogs I decided that I should try and install R from source again. I have a what seems like a very odd error, to me at least. I've followed the installation guide at http://r.research.att.com/building.html. I googled the link file 'libgomp.1.dylib' that seems to be causing the error and got stuff about openMPI. I reinstalled openMPI to check if this did anything, which it didn't. I've also tried using the configure parameter --disable-openmp also with no luck. :(
>
> Any ideas?
>
> Cheers,
>
> Paul
>
>>./configure SHELL='/bin/bash' r_arch=x86_64 CC="gcc -arch x86_64 -std=gnu99" CXX="g++ -arch x86_64" OBJC="gcc -arch x86_64" F77="gfortran -arch x86_64" FC="gfortran -arch x86_64" --with-system-zlib --with-blas='-framework vecLib' --with-lapack --with-tcltk --with-readline --enable-R-profiling --with-system-bzlib R_BROWSER='/Applications/Firefox.app/Contents/MacOS/firefox' R_PDFVIEWER='/Applications/Preview.app/Contents/MacOS/Preview' && \
> make -j4
> ....
> ....
> R is now configured for x86_64-apple-darwin10.7.0
>
>  Source directory:          .
>  Installation directory:    /Library/Frameworks
>
>  C compiler:                gcc -arch x86_64 -std=gnu99  -g -O2
>  Fortran 77 compiler:       gfortran -arch x86_64  -g -O2
>
>  C++ compiler:              g++ -arch x86_64  -g -O2
>  Fortran 90/95 compiler:    gfortran -arch x86_64 -g -O2
>  Obj-C compiler:     gcc -arch x86_64 -g -O2
>
>  Interfaces supported:      X11, aqua, tcltk
>  External libraries:        readline, BLAS(vecLib), LAPACK(in blas), ICU
>  Additional capabilities:   PNG, JPEG, NLS, cairo
>  Options enabled:           framework, R profiling, Java
>
>  Recommended packages:      yes
> ....
> ....
> make[3]: `libunix.a' is up to date.
> gcc -arch x86_64 -std=gnu99 -I. -I../../src/include -I../../src/include  -I/usr/local/include -DHAVE_CONFIG_H   -fopenmp -fPIC  -g -O2 -DR_HOME='"/Users/pbenton//R/R-2.13.0"' -o Rscript \
>  ./Rscript.c
> make[3]: `Makedeps' is up to date.
> /Users/pbenton/R/R-2.13.0/lib/x86_64/libR.dylib is unchanged
> /Users/pbenton/R/R-2.13.0/bin/exec/x86_64/R is unchanged
> make[4]: `Makedeps' is up to date.
> make[4]: `internet.so' is up to date.
> make[4]: `Makedeps' is up to date.
> make[4]: `lapack.so' is up to date.
> make[4]: `Makedeps' is up to date.
> make[4]: `vfonts.so' is up to date.
> make[4]: `Makedeps' is up to date.
> make[4]: `R_X11.so' is up to date.
> building system startup profile
> building package 'base'
> all.R is unchanged
> ../../../library/base/R/base is unchanged
> dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address
>  Referenced from: /usr/local/lib/libgomp.1.dylib
>  Expected in: /usr/local/lib/libgcc_s.1.dylib
>
> dyld: Symbol not found: ___emutls_get_address
>  Referenced from: /usr/local/lib/libgomp.1.dylib
>  Expected in: /usr/local/lib/libgcc_s.1.dylib
>
> /bin/bash: line 1: 92017 Done                    cat ./makebasedb.R
>     92018 Trace/BPT trap          | R_DEFAULT_PACKAGES=NULL LC_ALL=C ../../../bin/R --vanilla --slave > /dev/null
> make[3]: *** [all] Error 133
> make[2]: *** [R] Error 1
> make[1]: *** [R] Error 1
> make: *** [R] Error 1
>
>
> H. Paul Benton
> Graduate Student
>
>
>
>        [[alternative HTML version deleted]]
>
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